Starting phenix.real_space_refine on Thu Feb 5 01:25:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ia2_52778/02_2026/9ia2_52778.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ia2_52778/02_2026/9ia2_52778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ia2_52778/02_2026/9ia2_52778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ia2_52778/02_2026/9ia2_52778.map" model { file = "/net/cci-nas-00/data/ceres_data/9ia2_52778/02_2026/9ia2_52778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ia2_52778/02_2026/9ia2_52778.cif" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 4467 2.51 5 N 1224 2.21 5 O 1376 1.98 5 H 6758 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13854 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 714, 11268 Classifications: {'peptide': 714} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 685} Chain breaks: 7 Chain: "B" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 2432 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 154 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 2, 'TRANS': 7} Time building chain proxies: 2.70, per 1000 atoms: 0.19 Number of scatterers: 13854 At special positions: 0 Unit cell: (92.837, 81.141, 114.036, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 1376 8.00 N 1224 7.00 C 4467 6.00 H 6758 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 724 " distance=2.04 Simple disulfide: pdb=" SG CYS A 173 " - pdb=" SG CYS A 725 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 476.5 milliseconds 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1640 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 4 sheets defined 13.7% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 27 through 33 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 463 through 470 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 660 through 668 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 675 through 680 removed outlier: 4.595A pdb=" N ASN A 680 " --> pdb=" O GLU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 773 removed outlier: 3.503A pdb=" N MET A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 132 through 171 removed outlier: 3.644A pdb=" N ASP B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) Proline residue: B 160 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 69 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 69 through 69 current: chain 'A' and resid 81 through 87 Processing sheet with id=AA2, first strand: chain 'A' and resid 123 through 126 removed outlier: 4.360A pdb=" N LYS A 123 " --> pdb=" O TRP A 136 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 153 " --> pdb=" O ASP A 166 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 162 through 166 current: chain 'A' and resid 180 through 183 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 180 through 183 current: chain 'A' and resid 195 through 205 removed outlier: 6.880A pdb=" N ARG A 202 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR A 212 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LYS A 204 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 210 " --> pdb=" O LYS A 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 227 through 228 current: chain 'A' and resid 240 through 244 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 240 through 244 current: chain 'A' and resid 255 through 264 removed outlier: 3.668A pdb=" N MET A 264 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN A 269 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR A 356 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N VAL A 334 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 10.962A pdb=" N TYR A 354 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LYS A 375 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU A 391 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N PHE A 377 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER A 389 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N HIS A 416 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN A 393 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA A 414 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP A 395 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY A 412 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASN A 397 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 410 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR A 399 " --> pdb=" O THR A 408 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A 408 " --> pdb=" O TYR A 399 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASN A 401 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N PHE A 406 " --> pdb=" O ASN A 401 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 445 through 453 current: chain 'A' and resid 477 through 480 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 477 through 480 current: chain 'A' and resid 505 through 517 removed outlier: 3.800A pdb=" N VAL A 607 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TYR A 584 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N SER A 605 " --> pdb=" O TYR A 584 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 637 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASP A 629 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL A 635 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASP A 706 " --> pdb=" O GLN A 712 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLN A 712 " --> pdb=" O ASP A 706 " (cutoff:3.500A) removed outlier: 13.215A pdb=" N LYS A 711 " --> pdb=" O GLY A 738 " (cutoff:3.500A) removed outlier: 13.292A pdb=" N GLY A 738 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ALA A 713 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL A 747 " --> pdb=" O ASN A 737 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 63 removed outlier: 6.826A pdb=" N MET B 36 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU B 75 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE B 37 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU B 77 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASP B 39 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N LYS B 79 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU B 75 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU B 109 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU B 77 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR B 107 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 79 " --> pdb=" O ASN B 105 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU B 97 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL B 89 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR B 95 " --> pdb=" O VAL B 89 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 6756 1.12 - 1.29: 1227 1.29 - 1.47: 2830 1.47 - 1.65: 3156 1.65 - 1.82: 52 Bond restraints: 14021 Sorted by residual: bond pdb=" CD2 HIS A 90 " pdb=" HD2 HIS A 90 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" NH2 ARG A 615 " pdb="HH21 ARG A 615 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" CE2 TYR A 537 " pdb=" HE2 TYR A 537 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" CZ2 TRP A 311 " pdb=" HZ2 TRP A 311 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.74e+01 bond pdb=" NH2 ARG A 565 " pdb="HH22 ARG A 565 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.74e+01 ... (remaining 14016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 20551 2.35 - 4.70: 3587 4.70 - 7.04: 864 7.04 - 9.39: 110 9.39 - 11.74: 3 Bond angle restraints: 25115 Sorted by residual: angle pdb=" C TYR A 678 " pdb=" N LYS A 679 " pdb=" CA LYS A 679 " ideal model delta sigma weight residual 120.38 129.29 -8.91 1.37e+00 5.33e-01 4.23e+01 angle pdb=" CA ASP A 256 " pdb=" CB ASP A 256 " pdb=" CG ASP A 256 " ideal model delta sigma weight residual 112.60 118.59 -5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" CA HIS A 745 " pdb=" CB HIS A 745 " pdb=" CG HIS A 745 " ideal model delta sigma weight residual 113.80 119.36 -5.56 1.00e+00 1.00e+00 3.09e+01 angle pdb=" CA ASP A 568 " pdb=" CB ASP A 568 " pdb=" CG ASP A 568 " ideal model delta sigma weight residual 112.60 117.64 -5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" CA ASP A 105 " pdb=" CB ASP A 105 " pdb=" CG ASP A 105 " ideal model delta sigma weight residual 112.60 117.52 -4.92 1.00e+00 1.00e+00 2.42e+01 ... (remaining 25110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6135 17.90 - 35.79: 344 35.79 - 53.69: 113 53.69 - 71.59: 80 71.59 - 89.49: 10 Dihedral angle restraints: 6682 sinusoidal: 3578 harmonic: 3104 Sorted by residual: dihedral pdb=" C LYS A 131 " pdb=" N LYS A 131 " pdb=" CA LYS A 131 " pdb=" CB LYS A 131 " ideal model delta harmonic sigma weight residual -122.60 -138.41 15.81 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" N LYS A 131 " pdb=" C LYS A 131 " pdb=" CA LYS A 131 " pdb=" CB LYS A 131 " ideal model delta harmonic sigma weight residual 122.80 136.49 -13.69 0 2.50e+00 1.60e-01 3.00e+01 dihedral pdb=" CA TYR A 458 " pdb=" C TYR A 458 " pdb=" N GLN A 459 " pdb=" CA GLN A 459 " ideal model delta harmonic sigma weight residual 180.00 152.93 27.07 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 6679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 809 0.111 - 0.221: 208 0.221 - 0.332: 17 0.332 - 0.443: 2 0.443 - 0.553: 1 Chirality restraints: 1037 Sorted by residual: chirality pdb=" CA LYS A 131 " pdb=" N LYS A 131 " pdb=" C LYS A 131 " pdb=" CB LYS A 131 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CA ASN A 160 " pdb=" N ASN A 160 " pdb=" C ASN A 160 " pdb=" CB ASN A 160 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA GLU A 159 " pdb=" N GLU A 159 " pdb=" C GLU A 159 " pdb=" CB GLU A 159 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 1034 not shown) Planarity restraints: 2122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 465 " -0.217 2.00e-02 2.50e+03 9.07e-02 3.29e+02 pdb=" CG TRP A 465 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 465 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 465 " 0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP A 465 " 0.074 2.00e-02 2.50e+03 pdb=" CE2 TRP A 465 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 465 " 0.068 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 465 " -0.048 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 465 " 0.036 2.00e-02 2.50e+03 pdb=" CH2 TRP A 465 " -0.059 2.00e-02 2.50e+03 pdb=" HD1 TRP A 465 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP A 465 " 0.150 2.00e-02 2.50e+03 pdb=" HE3 TRP A 465 " 0.136 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 465 " -0.080 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 465 " 0.066 2.00e-02 2.50e+03 pdb=" HH2 TRP A 465 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 224 " 0.169 9.50e-02 1.11e+02 1.29e-01 3.05e+02 pdb=" NE ARG A 224 " 0.096 2.00e-02 2.50e+03 pdb=" CZ ARG A 224 " 0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG A 224 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 224 " 0.015 2.00e-02 2.50e+03 pdb="HH11 ARG A 224 " -0.216 2.00e-02 2.50e+03 pdb="HH12 ARG A 224 " 0.225 2.00e-02 2.50e+03 pdb="HH21 ARG A 224 " -0.047 2.00e-02 2.50e+03 pdb="HH22 ARG A 224 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 157 " -0.264 9.50e-02 1.11e+02 1.33e-01 2.33e+02 pdb=" NE ARG A 157 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG A 157 " -0.059 2.00e-02 2.50e+03 pdb=" NH1 ARG A 157 " -0.118 2.00e-02 2.50e+03 pdb=" NH2 ARG A 157 " -0.015 2.00e-02 2.50e+03 pdb="HH11 ARG A 157 " 0.227 2.00e-02 2.50e+03 pdb="HH12 ARG A 157 " -0.092 2.00e-02 2.50e+03 pdb="HH21 ARG A 157 " 0.086 2.00e-02 2.50e+03 pdb="HH22 ARG A 157 " 0.043 2.00e-02 2.50e+03 ... (remaining 2119 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1037 2.18 - 2.78: 23089 2.78 - 3.39: 37434 3.39 - 3.99: 52517 3.99 - 4.60: 75124 Nonbonded interactions: 189201 Sorted by model distance: nonbonded pdb=" OE1 GLU A 288 " pdb=" HH TYR A 347 " model vdw 1.573 2.450 nonbonded pdb=" OD2 ASP A 395 " pdb=" HH TYR A 411 " model vdw 1.600 2.450 nonbonded pdb=" OE2 GLU A 643 " pdb=" HH TYR A 780 " model vdw 1.611 2.450 nonbonded pdb=" HG SER A 80 " pdb=" OD2 ASP A 114 " model vdw 1.611 2.450 nonbonded pdb=" HG SER A 172 " pdb=" O ARG A 759 " model vdw 1.639 2.450 ... (remaining 189196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 0.270 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.030 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.043 7265 Z= 0.745 Angle : 1.782 8.914 9862 Z= 1.203 Chirality : 0.093 0.553 1037 Planarity : 0.016 0.143 1293 Dihedral : 13.118 89.485 2663 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 0.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.52 % Allowed : 1.82 % Favored : 97.66 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.26), residues: 857 helix: -0.19 (0.47), residues: 93 sheet: 1.00 (0.24), residues: 373 loop : -0.67 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 429 TYR 0.127 0.020 TYR A 347 PHE 0.076 0.010 PHE A 377 TRP 0.126 0.020 TRP A 465 HIS 0.010 0.003 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.01252 ( 7263) covalent geometry : angle 1.78171 ( 9858) SS BOND : bond 0.00419 ( 2) SS BOND : angle 2.81083 ( 4) hydrogen bonds : bond 0.13935 ( 301) hydrogen bonds : angle 7.14428 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 159 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8056 (mmm) cc_final: 0.7607 (mmm) REVERT: A 120 LYS cc_start: 0.7854 (mttt) cc_final: 0.7276 (mtpp) REVERT: A 132 ASP cc_start: 0.5977 (t0) cc_final: 0.5469 (m-30) REVERT: A 193 GLU cc_start: 0.6897 (mm-30) cc_final: 0.6676 (mm-30) REVERT: A 255 MET cc_start: 0.9039 (ptp) cc_final: 0.8834 (ptt) REVERT: A 296 LYS cc_start: 0.8187 (mttt) cc_final: 0.7867 (mppt) REVERT: A 459 GLN cc_start: 0.7365 (mt0) cc_final: 0.6935 (mt0) REVERT: A 476 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7859 (mm-30) REVERT: A 494 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7657 (mm-30) REVERT: A 499 MET cc_start: 0.7699 (mpp) cc_final: 0.7368 (ttt) REVERT: A 529 ASP cc_start: 0.8299 (p0) cc_final: 0.8029 (p0) REVERT: A 601 ASP cc_start: 0.8377 (m-30) cc_final: 0.8067 (m-30) REVERT: A 615 ARG cc_start: 0.7984 (ttt90) cc_final: 0.7420 (tpt-90) REVERT: A 619 ARG cc_start: 0.8097 (mtt180) cc_final: 0.7860 (mtm-85) REVERT: A 633 ASP cc_start: 0.7676 (t0) cc_final: 0.6934 (t0) REVERT: A 670 LYS cc_start: 0.8961 (tttt) cc_final: 0.8583 (mptm) REVERT: A 674 THR cc_start: 0.8975 (m) cc_final: 0.8598 (p) REVERT: A 754 PHE cc_start: 0.8534 (t80) cc_final: 0.7279 (m-80) REVERT: B 94 GLN cc_start: 0.7965 (mt0) cc_final: 0.7573 (mm-40) REVERT: B 109 LEU cc_start: 0.8749 (tt) cc_final: 0.8501 (tm) REVERT: B 145 LYS cc_start: 0.8712 (tttt) cc_final: 0.8382 (tmtt) outliers start: 4 outliers final: 1 residues processed: 162 average time/residue: 1.2490 time to fit residues: 213.0171 Evaluate side-chains 98 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN A 442 ASN A 513 GLN B 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.117854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.092644 restraints weight = 27967.928| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.01 r_work: 0.3240 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7265 Z= 0.163 Angle : 0.589 4.596 9862 Z= 0.323 Chirality : 0.046 0.144 1037 Planarity : 0.005 0.041 1293 Dihedral : 5.974 38.006 984 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.43 % Allowed : 8.19 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.27), residues: 857 helix: 1.10 (0.52), residues: 95 sheet: 0.54 (0.22), residues: 430 loop : -0.55 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 650 TYR 0.012 0.001 TYR A 537 PHE 0.009 0.001 PHE A 541 TRP 0.011 0.001 TRP A 465 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7263) covalent geometry : angle 0.58873 ( 9858) SS BOND : bond 0.00076 ( 2) SS BOND : angle 1.03419 ( 4) hydrogen bonds : bond 0.04460 ( 301) hydrogen bonds : angle 5.78072 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8130 (mmm) cc_final: 0.7757 (mmm) REVERT: A 120 LYS cc_start: 0.8080 (mttt) cc_final: 0.7499 (mtpp) REVERT: A 137 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8324 (mm-30) REVERT: A 202 ARG cc_start: 0.7082 (mtp85) cc_final: 0.6870 (mtm-85) REVERT: A 296 LYS cc_start: 0.8044 (mttt) cc_final: 0.7749 (mppt) REVERT: A 459 GLN cc_start: 0.7528 (mt0) cc_final: 0.7149 (mm110) REVERT: A 499 MET cc_start: 0.7674 (mpp) cc_final: 0.7443 (ttt) REVERT: A 599 ASN cc_start: 0.8319 (m-40) cc_final: 0.7217 (m110) REVERT: A 601 ASP cc_start: 0.8463 (m-30) cc_final: 0.8195 (m-30) REVERT: A 615 ARG cc_start: 0.8170 (ttt90) cc_final: 0.7754 (tpt-90) REVERT: A 670 LYS cc_start: 0.8590 (tttt) cc_final: 0.8309 (mptm) REVERT: A 674 THR cc_start: 0.8865 (m) cc_final: 0.8523 (p) REVERT: A 754 PHE cc_start: 0.8404 (t80) cc_final: 0.7277 (m-80) REVERT: A 757 GLU cc_start: 0.8073 (tt0) cc_final: 0.7836 (tt0) REVERT: B 28 GLN cc_start: 0.8609 (tp40) cc_final: 0.7935 (tp-100) REVERT: B 94 GLN cc_start: 0.8026 (mt0) cc_final: 0.7588 (mm110) REVERT: B 145 LYS cc_start: 0.8597 (tttt) cc_final: 0.8339 (tmtt) outliers start: 11 outliers final: 4 residues processed: 118 average time/residue: 1.4203 time to fit residues: 175.7302 Evaluate side-chains 94 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 132 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 67 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN A 684 GLN A 781 GLN B 53 ASN B 138 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.088314 restraints weight = 27977.068| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.96 r_work: 0.3183 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7265 Z= 0.161 Angle : 0.550 5.476 9862 Z= 0.300 Chirality : 0.046 0.151 1037 Planarity : 0.005 0.054 1293 Dihedral : 5.335 23.553 984 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.04 % Allowed : 9.75 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.27), residues: 857 helix: 1.54 (0.52), residues: 95 sheet: 0.47 (0.23), residues: 433 loop : -0.51 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.018 0.001 TYR A 537 PHE 0.009 0.001 PHE A 377 TRP 0.007 0.001 TRP A 465 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 7263) covalent geometry : angle 0.54975 ( 9858) SS BOND : bond 0.00090 ( 2) SS BOND : angle 0.92712 ( 4) hydrogen bonds : bond 0.04028 ( 301) hydrogen bonds : angle 5.47030 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8099 (mmm) cc_final: 0.7721 (mmm) REVERT: A 86 GLU cc_start: 0.8096 (tt0) cc_final: 0.7654 (tm-30) REVERT: A 120 LYS cc_start: 0.8290 (mttt) cc_final: 0.7667 (mtpp) REVERT: A 137 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8394 (mm-30) REVERT: A 183 VAL cc_start: 0.8602 (t) cc_final: 0.8317 (m) REVERT: A 202 ARG cc_start: 0.7311 (mtp85) cc_final: 0.6906 (mtm-85) REVERT: A 296 LYS cc_start: 0.8086 (mttt) cc_final: 0.7871 (mppt) REVERT: A 426 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7428 (mm-30) REVERT: A 459 GLN cc_start: 0.7866 (mt0) cc_final: 0.7408 (tp40) REVERT: A 494 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8232 (mt-10) REVERT: A 499 MET cc_start: 0.7756 (mpp) cc_final: 0.7518 (ptp) REVERT: A 599 ASN cc_start: 0.8458 (m-40) cc_final: 0.8213 (m110) REVERT: A 615 ARG cc_start: 0.8321 (ttt90) cc_final: 0.7980 (tpm170) REVERT: A 670 LYS cc_start: 0.8577 (tttt) cc_final: 0.8321 (mmtp) REVERT: A 674 THR cc_start: 0.8968 (m) cc_final: 0.8655 (p) REVERT: A 744 GLN cc_start: 0.8829 (mp-120) cc_final: 0.8509 (mp10) REVERT: B 94 GLN cc_start: 0.7980 (mt0) cc_final: 0.7525 (mm110) REVERT: B 145 LYS cc_start: 0.8561 (tttt) cc_final: 0.8302 (tmtt) outliers start: 8 outliers final: 5 residues processed: 97 average time/residue: 1.4564 time to fit residues: 148.1279 Evaluate side-chains 91 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain B residue 132 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.111345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.085908 restraints weight = 27966.695| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.00 r_work: 0.3142 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 7265 Z= 0.209 Angle : 0.546 5.035 9862 Z= 0.294 Chirality : 0.046 0.147 1037 Planarity : 0.005 0.046 1293 Dihedral : 5.180 18.678 983 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.56 % Allowed : 10.40 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.27), residues: 857 helix: 1.77 (0.51), residues: 97 sheet: 0.34 (0.23), residues: 433 loop : -0.77 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 429 TYR 0.019 0.001 TYR A 537 PHE 0.009 0.001 PHE A 211 TRP 0.006 0.001 TRP A 465 HIS 0.004 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 7263) covalent geometry : angle 0.54582 ( 9858) SS BOND : bond 0.00112 ( 2) SS BOND : angle 0.91296 ( 4) hydrogen bonds : bond 0.04005 ( 301) hydrogen bonds : angle 5.50853 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8089 (mmm) cc_final: 0.7743 (mmm) REVERT: A 86 GLU cc_start: 0.8183 (tt0) cc_final: 0.7692 (tm-30) REVERT: A 120 LYS cc_start: 0.8327 (mttt) cc_final: 0.7721 (mtpp) REVERT: A 127 ASN cc_start: 0.6871 (t0) cc_final: 0.6485 (t0) REVERT: A 161 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7429 (ttt-90) REVERT: A 183 VAL cc_start: 0.8617 (t) cc_final: 0.8270 (m) REVERT: A 193 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: A 202 ARG cc_start: 0.7513 (mtp85) cc_final: 0.7076 (mtm-85) REVERT: A 296 LYS cc_start: 0.8113 (mttt) cc_final: 0.7831 (mppt) REVERT: A 426 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8147 (mt-10) REVERT: A 459 GLN cc_start: 0.7902 (mt0) cc_final: 0.7507 (tp40) REVERT: A 461 THR cc_start: 0.8925 (m) cc_final: 0.8626 (p) REVERT: A 497 MET cc_start: 0.7667 (mmm) cc_final: 0.7086 (mtp) REVERT: A 499 MET cc_start: 0.7737 (mpp) cc_final: 0.7446 (ptp) REVERT: A 599 ASN cc_start: 0.8312 (m-40) cc_final: 0.7837 (m110) REVERT: A 615 ARG cc_start: 0.8322 (ttt90) cc_final: 0.7980 (tpm170) REVERT: A 670 LYS cc_start: 0.8587 (tttt) cc_final: 0.8317 (mmtp) REVERT: A 674 THR cc_start: 0.9017 (m) cc_final: 0.8708 (p) REVERT: A 749 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7781 (t70) REVERT: B 94 GLN cc_start: 0.7937 (mt0) cc_final: 0.7515 (mm110) REVERT: B 145 LYS cc_start: 0.8546 (tttt) cc_final: 0.8286 (tmtt) outliers start: 12 outliers final: 7 residues processed: 95 average time/residue: 1.3804 time to fit residues: 138.0656 Evaluate side-chains 91 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 171 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.111099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.085620 restraints weight = 28078.472| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.02 r_work: 0.3139 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7265 Z= 0.202 Angle : 0.531 5.325 9862 Z= 0.286 Chirality : 0.046 0.149 1037 Planarity : 0.005 0.047 1293 Dihedral : 5.061 18.138 983 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.69 % Allowed : 11.31 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.27), residues: 857 helix: 1.98 (0.52), residues: 97 sheet: 0.32 (0.24), residues: 415 loop : -0.74 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 421 TYR 0.019 0.001 TYR A 537 PHE 0.010 0.001 PHE A 377 TRP 0.006 0.001 TRP A 272 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 7263) covalent geometry : angle 0.53036 ( 9858) SS BOND : bond 0.00130 ( 2) SS BOND : angle 0.85400 ( 4) hydrogen bonds : bond 0.03856 ( 301) hydrogen bonds : angle 5.43843 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8038 (mmm) cc_final: 0.7729 (mmm) REVERT: A 33 LEU cc_start: 0.8142 (tp) cc_final: 0.7745 (mm) REVERT: A 120 LYS cc_start: 0.8370 (mttt) cc_final: 0.7811 (mtpp) REVERT: A 127 ASN cc_start: 0.6939 (t0) cc_final: 0.6588 (t0) REVERT: A 154 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7896 (mtm) REVERT: A 183 VAL cc_start: 0.8578 (t) cc_final: 0.8197 (m) REVERT: A 202 ARG cc_start: 0.7579 (mtp85) cc_final: 0.7119 (mtm-85) REVERT: A 296 LYS cc_start: 0.8121 (mttt) cc_final: 0.7784 (mppt) REVERT: A 459 GLN cc_start: 0.7865 (mt0) cc_final: 0.7524 (tp40) REVERT: A 461 THR cc_start: 0.8920 (m) cc_final: 0.8639 (p) REVERT: A 471 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8534 (m) REVERT: A 497 MET cc_start: 0.7793 (mmm) cc_final: 0.7331 (mtp) REVERT: A 499 MET cc_start: 0.7775 (mpp) cc_final: 0.7419 (ptp) REVERT: A 599 ASN cc_start: 0.8368 (m-40) cc_final: 0.7955 (m110) REVERT: A 615 ARG cc_start: 0.8302 (ttt90) cc_final: 0.7950 (tpm170) REVERT: A 670 LYS cc_start: 0.8595 (tttt) cc_final: 0.8343 (mmtp) REVERT: A 674 THR cc_start: 0.9048 (m) cc_final: 0.8747 (p) REVERT: B 94 GLN cc_start: 0.7970 (mt0) cc_final: 0.7558 (mm-40) REVERT: B 145 LYS cc_start: 0.8537 (tttt) cc_final: 0.8265 (tmtt) outliers start: 13 outliers final: 6 residues processed: 89 average time/residue: 1.2920 time to fit residues: 121.4037 Evaluate side-chains 87 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 169 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.111365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.086016 restraints weight = 27893.848| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.01 r_work: 0.3141 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7265 Z= 0.184 Angle : 0.515 4.991 9862 Z= 0.277 Chirality : 0.045 0.148 1037 Planarity : 0.005 0.048 1293 Dihedral : 4.953 17.851 983 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.82 % Allowed : 11.83 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.27), residues: 857 helix: 2.10 (0.52), residues: 97 sheet: 0.23 (0.24), residues: 415 loop : -0.75 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.018 0.001 TYR A 537 PHE 0.009 0.001 PHE A 377 TRP 0.006 0.001 TRP A 272 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 7263) covalent geometry : angle 0.51467 ( 9858) SS BOND : bond 0.00130 ( 2) SS BOND : angle 0.76921 ( 4) hydrogen bonds : bond 0.03738 ( 301) hydrogen bonds : angle 5.37841 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8024 (mmm) cc_final: 0.7679 (mmm) REVERT: A 33 LEU cc_start: 0.8165 (tp) cc_final: 0.7777 (mm) REVERT: A 120 LYS cc_start: 0.8348 (mttt) cc_final: 0.7766 (mtpp) REVERT: A 127 ASN cc_start: 0.7012 (t0) cc_final: 0.6640 (t0) REVERT: A 183 VAL cc_start: 0.8543 (t) cc_final: 0.8132 (m) REVERT: A 202 ARG cc_start: 0.7621 (mtp85) cc_final: 0.7124 (mtm-85) REVERT: A 296 LYS cc_start: 0.8176 (mttt) cc_final: 0.7770 (mppt) REVERT: A 459 GLN cc_start: 0.7902 (mt0) cc_final: 0.7556 (tp40) REVERT: A 461 THR cc_start: 0.8933 (m) cc_final: 0.8659 (p) REVERT: A 497 MET cc_start: 0.7880 (mmm) cc_final: 0.7472 (mtp) REVERT: A 499 MET cc_start: 0.7826 (mpp) cc_final: 0.7442 (ptp) REVERT: A 615 ARG cc_start: 0.8262 (ttt90) cc_final: 0.7942 (tpm170) REVERT: A 670 LYS cc_start: 0.8610 (tttt) cc_final: 0.8346 (mmtp) REVERT: A 674 THR cc_start: 0.9051 (m) cc_final: 0.8779 (p) REVERT: A 749 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7856 (t0) REVERT: B 94 GLN cc_start: 0.7989 (mt0) cc_final: 0.7524 (mm110) REVERT: B 145 LYS cc_start: 0.8528 (tttt) cc_final: 0.8256 (tmtt) outliers start: 14 outliers final: 8 residues processed: 86 average time/residue: 1.2565 time to fit residues: 114.2945 Evaluate side-chains 89 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 171 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 65 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.112463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.087240 restraints weight = 27691.702| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.01 r_work: 0.3159 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7265 Z= 0.127 Angle : 0.484 4.840 9862 Z= 0.259 Chirality : 0.045 0.146 1037 Planarity : 0.004 0.048 1293 Dihedral : 4.741 17.012 983 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.78 % Allowed : 12.61 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.27), residues: 857 helix: 2.34 (0.53), residues: 96 sheet: 0.20 (0.24), residues: 415 loop : -0.67 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 421 TYR 0.016 0.001 TYR A 537 PHE 0.007 0.001 PHE A 575 TRP 0.005 0.001 TRP A 272 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7263) covalent geometry : angle 0.48417 ( 9858) SS BOND : bond 0.00098 ( 2) SS BOND : angle 0.99021 ( 4) hydrogen bonds : bond 0.03445 ( 301) hydrogen bonds : angle 5.24174 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8035 (mmm) cc_final: 0.7687 (mmm) REVERT: A 33 LEU cc_start: 0.8151 (tp) cc_final: 0.7767 (mm) REVERT: A 120 LYS cc_start: 0.8320 (mttt) cc_final: 0.7758 (mtpp) REVERT: A 127 ASN cc_start: 0.7020 (t0) cc_final: 0.6634 (t0) REVERT: A 183 VAL cc_start: 0.8521 (t) cc_final: 0.8128 (m) REVERT: A 202 ARG cc_start: 0.7591 (mtp85) cc_final: 0.7068 (mtp180) REVERT: A 295 ASP cc_start: 0.8405 (t0) cc_final: 0.8179 (t0) REVERT: A 296 LYS cc_start: 0.8183 (mttt) cc_final: 0.7769 (mppt) REVERT: A 459 GLN cc_start: 0.7865 (mt0) cc_final: 0.7548 (tp40) REVERT: A 461 THR cc_start: 0.8915 (m) cc_final: 0.8657 (p) REVERT: A 497 MET cc_start: 0.7791 (mmm) cc_final: 0.7437 (mtp) REVERT: A 499 MET cc_start: 0.7848 (mpp) cc_final: 0.7389 (ptp) REVERT: A 599 ASN cc_start: 0.8093 (m110) cc_final: 0.7813 (m110) REVERT: A 615 ARG cc_start: 0.8261 (ttt90) cc_final: 0.7894 (tpm170) REVERT: A 670 LYS cc_start: 0.8607 (tttt) cc_final: 0.8329 (mmtp) REVERT: A 674 THR cc_start: 0.9040 (m) cc_final: 0.8782 (p) REVERT: A 744 GLN cc_start: 0.8891 (mp-120) cc_final: 0.8519 (mp10) REVERT: B 94 GLN cc_start: 0.7936 (mt0) cc_final: 0.7526 (mm-40) REVERT: B 145 LYS cc_start: 0.8495 (tttt) cc_final: 0.8225 (tmtt) outliers start: 6 outliers final: 5 residues processed: 91 average time/residue: 1.3113 time to fit residues: 125.9513 Evaluate side-chains 88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain B residue 132 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 770 GLN B 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.112078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.086829 restraints weight = 27603.414| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.01 r_work: 0.3152 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7265 Z= 0.149 Angle : 0.494 4.762 9862 Z= 0.264 Chirality : 0.045 0.146 1037 Planarity : 0.004 0.048 1293 Dihedral : 4.707 16.790 983 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.04 % Allowed : 12.74 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.28), residues: 857 helix: 2.61 (0.53), residues: 95 sheet: 0.18 (0.24), residues: 415 loop : -0.72 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 421 TYR 0.016 0.001 TYR A 537 PHE 0.008 0.001 PHE A 575 TRP 0.006 0.001 TRP A 272 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7263) covalent geometry : angle 0.49368 ( 9858) SS BOND : bond 0.00047 ( 2) SS BOND : angle 0.96096 ( 4) hydrogen bonds : bond 0.03507 ( 301) hydrogen bonds : angle 5.21714 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8022 (mmm) cc_final: 0.7701 (mmm) REVERT: A 33 LEU cc_start: 0.8159 (tp) cc_final: 0.7791 (mm) REVERT: A 120 LYS cc_start: 0.8313 (mttt) cc_final: 0.7742 (mtpp) REVERT: A 127 ASN cc_start: 0.7022 (t0) cc_final: 0.6708 (t0) REVERT: A 183 VAL cc_start: 0.8529 (t) cc_final: 0.8125 (m) REVERT: A 185 SER cc_start: 0.9171 (m) cc_final: 0.8800 (p) REVERT: A 202 ARG cc_start: 0.7611 (mtp85) cc_final: 0.7062 (mtp180) REVERT: A 211 PHE cc_start: 0.7441 (t80) cc_final: 0.7236 (t80) REVERT: A 296 LYS cc_start: 0.8234 (mttt) cc_final: 0.7707 (mmtm) REVERT: A 459 GLN cc_start: 0.7840 (mt0) cc_final: 0.7553 (tp40) REVERT: A 461 THR cc_start: 0.8916 (m) cc_final: 0.8665 (p) REVERT: A 497 MET cc_start: 0.7892 (mmm) cc_final: 0.7648 (mtp) REVERT: A 599 ASN cc_start: 0.8018 (m110) cc_final: 0.7765 (m110) REVERT: A 615 ARG cc_start: 0.8264 (ttt90) cc_final: 0.7893 (tpm170) REVERT: A 670 LYS cc_start: 0.8599 (tttt) cc_final: 0.8327 (mmtp) REVERT: A 674 THR cc_start: 0.9041 (m) cc_final: 0.8784 (p) REVERT: A 744 GLN cc_start: 0.8909 (mp-120) cc_final: 0.8493 (mp10) REVERT: B 94 GLN cc_start: 0.7948 (mt0) cc_final: 0.7538 (mm-40) REVERT: B 145 LYS cc_start: 0.8509 (tttt) cc_final: 0.8238 (tmtt) outliers start: 8 outliers final: 6 residues processed: 91 average time/residue: 1.2845 time to fit residues: 123.4882 Evaluate side-chains 90 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain B residue 132 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 51 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.112137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.086840 restraints weight = 27848.225| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.01 r_work: 0.3153 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7265 Z= 0.154 Angle : 0.493 4.703 9862 Z= 0.264 Chirality : 0.045 0.146 1037 Planarity : 0.004 0.047 1293 Dihedral : 4.684 16.649 983 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.78 % Allowed : 13.00 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.28), residues: 857 helix: 2.56 (0.54), residues: 96 sheet: 0.17 (0.24), residues: 415 loop : -0.68 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 421 TYR 0.017 0.001 TYR A 537 PHE 0.008 0.001 PHE A 377 TRP 0.006 0.001 TRP A 272 HIS 0.002 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 7263) covalent geometry : angle 0.49289 ( 9858) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.90749 ( 4) hydrogen bonds : bond 0.03500 ( 301) hydrogen bonds : angle 5.21398 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8022 (mmm) cc_final: 0.7685 (mmm) REVERT: A 33 LEU cc_start: 0.8155 (tp) cc_final: 0.7807 (mm) REVERT: A 120 LYS cc_start: 0.8324 (mttt) cc_final: 0.7749 (mtpp) REVERT: A 127 ASN cc_start: 0.7072 (t0) cc_final: 0.6750 (t0) REVERT: A 183 VAL cc_start: 0.8516 (t) cc_final: 0.8106 (m) REVERT: A 185 SER cc_start: 0.9175 (m) cc_final: 0.8808 (p) REVERT: A 202 ARG cc_start: 0.7630 (mtp85) cc_final: 0.7067 (mtp180) REVERT: A 296 LYS cc_start: 0.8289 (mttt) cc_final: 0.7745 (mmtm) REVERT: A 459 GLN cc_start: 0.7860 (mt0) cc_final: 0.7591 (tp40) REVERT: A 461 THR cc_start: 0.8919 (m) cc_final: 0.8673 (p) REVERT: A 599 ASN cc_start: 0.8009 (m110) cc_final: 0.7754 (m110) REVERT: A 615 ARG cc_start: 0.8265 (ttt90) cc_final: 0.7891 (tpm170) REVERT: A 670 LYS cc_start: 0.8598 (tttt) cc_final: 0.8328 (mmtp) REVERT: A 674 THR cc_start: 0.9046 (m) cc_final: 0.8788 (p) REVERT: A 744 GLN cc_start: 0.8889 (mp-120) cc_final: 0.8479 (mp10) REVERT: B 94 GLN cc_start: 0.7934 (mt0) cc_final: 0.7501 (mm110) REVERT: B 145 LYS cc_start: 0.8511 (tttt) cc_final: 0.8238 (tmtt) outliers start: 6 outliers final: 7 residues processed: 88 average time/residue: 1.2959 time to fit residues: 120.3959 Evaluate side-chains 92 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 171 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 10 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.0050 chunk 69 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.112210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.086927 restraints weight = 27782.915| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.01 r_work: 0.3157 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7265 Z= 0.130 Angle : 0.489 5.088 9862 Z= 0.260 Chirality : 0.045 0.147 1037 Planarity : 0.004 0.047 1293 Dihedral : 4.632 16.462 983 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.78 % Allowed : 13.00 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.28), residues: 857 helix: 2.72 (0.54), residues: 95 sheet: 0.16 (0.25), residues: 412 loop : -0.70 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 421 TYR 0.016 0.001 TYR A 537 PHE 0.008 0.001 PHE A 377 TRP 0.006 0.001 TRP A 272 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7263) covalent geometry : angle 0.48836 ( 9858) SS BOND : bond 0.00067 ( 2) SS BOND : angle 0.83373 ( 4) hydrogen bonds : bond 0.03402 ( 301) hydrogen bonds : angle 5.17776 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.8022 (mmm) cc_final: 0.7679 (mmm) REVERT: A 33 LEU cc_start: 0.8140 (tp) cc_final: 0.7792 (mm) REVERT: A 120 LYS cc_start: 0.8323 (mttt) cc_final: 0.7752 (mtpp) REVERT: A 127 ASN cc_start: 0.7099 (t0) cc_final: 0.6778 (t0) REVERT: A 183 VAL cc_start: 0.8521 (t) cc_final: 0.8103 (m) REVERT: A 185 SER cc_start: 0.9173 (m) cc_final: 0.8804 (p) REVERT: A 202 ARG cc_start: 0.7636 (mtp85) cc_final: 0.7077 (mtp180) REVERT: A 296 LYS cc_start: 0.8303 (mttt) cc_final: 0.7739 (mmtm) REVERT: A 459 GLN cc_start: 0.7863 (mt0) cc_final: 0.7598 (tp40) REVERT: A 461 THR cc_start: 0.8911 (m) cc_final: 0.8673 (p) REVERT: A 599 ASN cc_start: 0.8003 (m110) cc_final: 0.7752 (m110) REVERT: A 615 ARG cc_start: 0.8255 (ttt90) cc_final: 0.7901 (tpm170) REVERT: A 670 LYS cc_start: 0.8601 (tttt) cc_final: 0.8325 (mmtp) REVERT: A 674 THR cc_start: 0.9040 (m) cc_final: 0.8789 (p) REVERT: A 744 GLN cc_start: 0.8904 (mp-120) cc_final: 0.8484 (mp10) REVERT: B 94 GLN cc_start: 0.7929 (mt0) cc_final: 0.7511 (mm110) REVERT: B 145 LYS cc_start: 0.8508 (tttt) cc_final: 0.8235 (tmtt) outliers start: 6 outliers final: 5 residues processed: 87 average time/residue: 1.3128 time to fit residues: 120.4768 Evaluate side-chains 88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain B residue 132 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 22 optimal weight: 0.0060 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 680 ASN A 745 HIS B 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.089452 restraints weight = 27951.921| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.00 r_work: 0.3193 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7265 Z= 0.099 Angle : 0.464 4.767 9862 Z= 0.245 Chirality : 0.044 0.143 1037 Planarity : 0.004 0.047 1293 Dihedral : 4.405 16.621 983 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.52 % Allowed : 13.26 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.28), residues: 857 helix: 2.82 (0.53), residues: 95 sheet: 0.16 (0.25), residues: 410 loop : -0.56 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 421 TYR 0.014 0.001 TYR A 537 PHE 0.007 0.001 PHE A 377 TRP 0.005 0.001 TRP A 125 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 7263) covalent geometry : angle 0.46368 ( 9858) SS BOND : bond 0.00075 ( 2) SS BOND : angle 0.71761 ( 4) hydrogen bonds : bond 0.03063 ( 301) hydrogen bonds : angle 4.98957 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5562.93 seconds wall clock time: 94 minutes 58.36 seconds (5698.36 seconds total)